Class Bio::Phylip::DistanceMatrix
In: lib/bio/appl/phylip/distance_matrix.rb
Parent: Object

This is a parser class for phylip distance matrix data created by dnadist, protdist, or restdist commands.

Methods

generate   new  

Attributes

matrix  [R]  distance matrix (returns Ruby‘s Matrix object)
original_matrix  [R]  matrix contains values as original strings. Use it when you doubt precision of floating-point numbers.
otu_names  [R]  names of OTUs
otus  [R]  number of OTUs

Public Class methods

generate(matrix, otu_names = nil, options = {})

Generates a new phylip distance matrix formatted text as a string.

[Source]

    # File lib/bio/appl/phylip/distance_matrix.rb, line 69
69:       def self.generate(matrix, otu_names = nil, options = {})
70:         if matrix.row_size != matrix.column_size then
71:           raise "must be a square matrix"
72:         end
73:         otus = matrix.row_size
74:         names = (0...otus).collect do |i|
75:           name = ((otu_names and otu_names[i]) or "OTU#{i.to_s}")
76:           name
77:         end
78:         data = (0...otus).collect do |i|
79:           x = (0...otus).collect { |j|  sprintf("%9.6f", matrix[i, j]) }
80:           x.unshift(sprintf("%-10s", names[i])[0, 10])
81: 
82:           str = x[0, 7].join(' ') + "\n"
83:           7.step(otus + 1, 7) do |k|
84:             str << ' ' + x[k, 7].join(' ') + "\n"
85:           end
86:           str
87:         end
88:         sprintf("%5d\n", otus) + data.join('')
89:       end
new(str)

creates a new distance matrix object

[Source]

    # File lib/bio/appl/phylip/distance_matrix.rb, line 27
27:       def initialize(str)
28:         data = str.strip.split(/(?:\r\n|\r|\n)/)
29:         @otus = data.shift.to_s.strip.to_i
30:         prev = nil
31:         data.collect! do |x|
32:           if /\A +/ =~ x and prev then
33:             prev.concat x.strip.split(/\s+/)
34:             nil
35:           else
36:             prev = x.strip.split(/\s+/)
37:             prev
38:           end
39:         end
40:         data.compact!
41:         if data.size != @otus then
42:           raise "inconsistent data (OTUs=#{@otus} but #{data.size} rows)"
43:         end
44:         @otu_names = data.collect { |x| x.shift }
45:         mat = data.collect do |x|
46:           if x.size != @otus then
47:             raise "inconsistent data (OTUs=#{@otus} but #{x.size} columns)"
48:           end
49:           x.collect { |y| y.to_f }
50:         end
51:         @matrix = Matrix.rows(mat, false)
52:         @original_matrix = Matrix.rows(data, false)
53:       end

[Validate]